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- PDB-8h63: Crystal structure of Internalin A from Listeria monocytogenes wit... -

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Basic information

Entry
Database: PDB / ID: 8h63
TitleCrystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound
Components
  • Internalin A
  • VHH10
KeywordsCELL INVASION/IMMUNE SYSTEM / Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / extracellular region
Similarity search - Function
: / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like ...: / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Internalin A
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCaaveiro, J.M.M. / Nagatoish, S. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H02420 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.
Authors: Yamazaki, T. / Nagatoishi, S. / Yamawaki, T. / Nozawa, T. / Matsunaga, R. / Nakakido, M. / Caaveiro, J.M.M. / Nakagawa, I. / Tsumoto, K.
History
DepositionOct 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Internalin A
B: VHH10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1999
Polymers62,6472
Non-polymers5527
Water13,745763
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.581, 52.420, 103.060
Angle α, β, γ (deg.)90.000, 128.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1083-

HOH

21A-1119-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Internalin A


Mass: 49914.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: inlA, lmo0433,intlA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DJM0
#2: Antibody VHH10


Mass: 12732.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 770 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.085 M HEPES sodium pH 7.0; 8.5% Isopropanol; 20% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→33.3 Å / Num. obs: 91994 / % possible obs: 96.6 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Net I/σ(I): 11.4
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12582 / CC1/2: 0.752 / Rpim(I) all: 0.294 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H62 6JB9

8h62

6jb9


Resolution: 1.53→31.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.412 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2266 2.5 %RANDOM
Rwork0.161 ---
obs0.1617 89716 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.15 Å2 / Biso mean: 15.245 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20.2 Å2
2---0.03 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.53→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 40 772 5203
Biso mean--25.01 26.58 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174284
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6426336
X-RAY DIFFRACTIONr_angle_other_deg1.5011.57110046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1925629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.19726.25200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.515799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1261511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025156
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02781
LS refinement shellResolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 159 -
Rwork0.255 5889 -
all-6048 -
obs--86.23 %

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